2015 DOE JGI’s science portfolio delves deeper into the Earth’s data mine

The U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility, has announced that 32 new projects have been selected for the 2015 Community Science Program (CSP). From sampling Antarctic lakes to Caribbean waters, and from plant root micro-ecosystems, to the subsurface underneath the water table in forested watersheds, the CSP 2015 projects portfolio highlights diverse environments where DOE mission-relevant science can be extracted.

“These projects catalyze JGI’s strategic shift in emphasis from solving an organism’s genome sequence to enabling an understanding of what this information enables organisms to do,” said Jim Bristow, DOE JGI Science Deputy who oversees the CSP. “To accomplish this, the projects selected combine DNA sequencing with large-scale experimental and computational capabilities, and in some cases include JGI’s new capability to write DNA in addition to reading it. These projects will expand research communities, and help to meet the DOE JGI imperative to translate sequence to function and ultimately into solutions for major energy and environmental problems.”

The CSP 2015 projects were selected by an external review panel from 76 full proposals received that resulted from 85 letters of intent submitted. The total allocation for the CSP 2015 portfolio is expected to exceed 60 trillion bases (terabases or Tb)-or the equivalent of 20,000 human genomes of plant, fungal and microbial genome sequences. The full list of projects may be found at http://jgi.doe.gov/our-projects/csp-plans/fy-2015-csp-plans/. The DOE JGI Community Science Program also accepts proposals for smaller-scale microbial, resequencing and DNA synthesis projects and reviews them twice a year. The CSP advances projects that harness DOE JGI’s capability in massive-scale DNA sequencing, analysis and synthesis in support of the DOE missions in alternative energy, global carbon cycling, and biogeochemistry.

Among the CSP 2015 projects selected is one from Regina Lamendella of Juniata College, who will investigate how microbial communities in Marcellus shale, the country’s largest shale gas field, respond to hydraulic fracturing and natural gas extraction. For example, as fracking uses chemicals, researchers are interested in how the microbial communities can break down environmental contaminants, and how they respond to the release of methane during oil extraction operations.

Some 1,500 miles south from those gas extraction sites, Monica Medina-Munoz of Penn State University will study the effect of thermal stress on the Caribbean coral Orbicella faveolata and the metabolic contribution of its coral host Symbiodinium. The calcium carbonate in coral reefs acts as carbon sinks, but reef health depends on microbial communities. If the photosynthetic symbionts are removed from the coral host, for example, the corals can die and calcification rates decrease. Understanding how to maintain stability in the coral-microbiome community can provide information on the coral’s contribution to the global ocean carbon cycle.

Longtime DOE JGI collaborator Jill Banfield of the University of California (UC), Berkeley is profiling the diversity of microbial communities found in the subsurface from the Rifle aquifer adjacent to the Colorado River. The subsurface is a massive, yet poorly understood, repository of organic carbon as well as greenhouse gases. Another research question, based on having the microbial populations close to both the water table and the river, is how they impact carbon, nitrogen and sulfur cycles. Her project is part of the first coordinated attempt to quantify the metabolic potential of an entire subsurface ecosystem under the aegis of the Lawrence Berkeley National Laboratory’s Subsurface Biogeochemistry Scientific Focus Area.

Banfield also successfully competed for a second CSP project to characterize the tree-root microbial interactions that occur below the soil mantle in the unsaturated zone or vadose zone, which extends into unweathered bedrock. The project’s goal is to understand how microbial communities this deep underground influence tree-based carbon fixation in forested watersheds by the Eel River in northwestern California.

Several fungal projects were selected for the 2015 CSP portfolio, including one led by Kabir Peay of Stanford University. He and his colleagues will study how fungal communities in animal feces decompose organic matter. His project has a stated end goal of developing a model system that emulates the ecosystem at Point Reyes National Seashore, where Tule elk are the largest native herbivores.

Another selected fungal project comes from Timothy James of University of Michigan, who will explore the so-called “dark matter fungi” – those not represented in culture collections. By sequencing several dozen species of unculturable zoosporic fungi from freshwater, soils and animal feces, he and his colleagues hope to develop a kingdom-wide fungal phylogenetic framework.

Christian Wurzbacher of Germany’s the Leibniz Institute of Freshwater Ecology and Inland Fisheries, IGB, will characterize fungi from the deep sea to peatlands to freshwater streams to understand the potentially novel adaptations that are necessary to thrive in their aquatic environments. The genomic information would provide information on their metabolic capabilities for breaking down cellulose, lignin and other plant cell wall components, and animal polymers such as keratin and chitin.

Many of the selected projects focus on DOE JGI Flagship Plant Genomes, with most centered on the poplar (Populus trichocarpa.) For example, longtime DOE JGI collaborator Steve DiFazio of West Virginia University is interested in poplar but will study its reproductive development with the help of a close relative, the willow (Salix purpurea). With its shorter generation time, the plant is a good model system and comparator for understanding sex determination, which can help bioenergy crop breeders by, for example, either accelerating or preventing flowering.

Another project comes from Posy Busby of the University of Washington, who will study the interactions between the poplar tree and its fungal, non-pathogenic symbionts or endophytes. As disease-causing pathogens interact with endophytes in leaves, he noted in his proposal, understanding the roles and functions of endophytes could prove useful to meeting future fuel and food requirements.

Along the lines of poplar endophytes, Carolin Frank at UC Merced will investigate the nitrogen-fixing endophytes in poplar, willow, and pine, with the aim of improving growth in grasses and agricultural crops under nutrient-poor conditions.

Rotem Sorek from the Weizmann Institute of Science in Israel takes a different approach starting from the hypothesis that poplar trees have an adaptive immunity system rooted in genome-encoded immune memory. Through deep sequencing of tissues from single poplar trees (some over a century old, others younger) his team hopes to gain insights into the tree genome’s short-term evolution and how its gene expression profiles change over time, as well as to predict how trees might respond under various climate change scenarios.

Tackling a different DOE JGI Flagship Plant Genome, Debbie Laudencia-Chingcuangco of the USDA-ARS will develop a genome-wide collection of several thousand mutants of the model grass Brachypodium distachyon to help domesticate the grasses that are being considered as candidate bioenergy feedstocks. This work is being done in collaboration with researchers at the Great Lakes Bioenergy Research Center, as the team there considers Brachypodium “critical to achieving its mission of developing productive energy crops that can be easily processed into fuels.”

Continuing the theme of candidate bioenergy grasses, Kankshita Swaminathan from the University of Illinois will study gene expression in polyploidy grasses Miscanthus and sugarcane, comparing them against the closely related diploid grass sorghum to understand how these plants recycle nutrients.

Baohong Zhang of East Carolina University also focused on a bioenergy grass, and his project will look at the microRNAs in switchgrass. These regulatory molecules are each just a couple dozen nucleotides in length and can downregulate (decrease the quantity of) a cellular component. With a library of these small transcripts, he and his team hope to identify the gene expression variation associated with desirable biofuel traits in switchgrass such as increased biomass and responses to drought and salinity stressors.

Nitin Baliga of the Institute of Systems Biology will use DOE JGI genome sequences to build a working model of the networks that regulate lipid accumulation in Chlamydomonas reinhardtii, still another DOE JGI Plant Flagship Genome and a model for characterizing biofuel production by algae.

Other accepted projects include:

The study of the genomes of 32 fungi of the Agaricales order, including 16 fungi to be sequenced for the first time, will be carried out by Jose Maria Barrasa of Spain’s University of Alcala. While many of the basidiomycete fungi involved in wood degradation that have been sequenced are from the Polyporales, he noted in his proposal, many of the fungi involved in breaking down leaf litter and buried wood are from the order Agaricales.

Now at the University of Connecticut, Jonathan Klassen conducted postdoctoral studies at GLBRC researcher Cameron Currie’s lab at University of Wisconsin-Madison. His project will study interactions in ant-microbial community fungus gardens in three states to learn more about how the associated bacterial metagenomes contribute to carbon and nitrogen cycling.

Hinsby Cadillo-Quiroz, at Arizona State University, will conduct a study of the microbial communities in the Amazon peatlands to understand their roles in both emitting greenhouse gases and in storing and cycling carbon. The peatlands are hotspots of soil organic carbon accumulation, and in the tropical regions, they are estimated to hold between 11 percent and 14 percent, or nearly 90 gigatons, of the global carbon stored in soils.

Barbara Campbell, Clemson University will study carbon cycling mechanisms of active bacteria and associated viruses in the freshwater to marine transition zone of the Delaware Bay. Understanding the microbes’ metabolism would help researchers understand they capabilities with regard to dealing with contaminants, and their roles in the nitrogen, sulfur and carbon cycles.

Jim Fredrickson of Pacific Northwest National Laboratory will characterize functional profiles of microbial mats in California, Washington and Yellowstone National Park to understand various functions such as how they produce hydrogen and methane, and break down cellulose.

Joyce Loper of USDA-ARS will carry out a comparative analysis of all Pseudomonas bacteria getting from DOE JGI the sequences of just over 100 type strains to infer a evolutionary history of the this genus — a phylogeny — to characterize the genomic diversity, and determine the distribution of genes linked to key observable traits in this non-uniform group of bacteria.

Holly Simon of Oregon Health & Science University is studying microbial populations in the Columbia River estuary, in part to learn how they enhance greenhouse gas CO2 methane and nitrous oxide production.

Michael Thon from Spain’s University of Salamanca will explore sequences of strains of the Colletotrichum species complex, which include fungal pathogens that infect many crops. One of the questions he and his team will ask is how these fungal strains have adapted to break down the range of plant cell wall compositions.

Kathleen Treseder of UC Irvine will study genes involved in sensitivity to higher temperatures in fungi from a warming experiment in an Alaskan boreal forest. The team’s plan is to fold the genomic information gained into a trait-based ecosystem model called DEMENT to predict carbon dioxide emissions under global warming.

Mary Wildermuth of UC Berkeley will study nearly a dozen genomes of powdery mildew fungi, including three that infect designated bioenergy crops. The project will identify the mechanisms by which the fungi successfully infect plants, information that could lead to the development of crops with improved resistance to fungal infection and limiting fungicide use to allow more sustainable agricultural practices.

Several researchers who have previously collaborated with the DOE JGI have new projects:

Ludmila Chistoserdova from the University of Washington had a pioneering collaboration with the DOE JGI to study microbial communities in Lake Washington. In her new project, she and her team will look at the microbes in the Lake Washington sediment to understand their role in metabolizing the potent greenhouse gas methane.

Rick Cavicchioli of Australia’s University of New South Wales will track how microbial communities change throughout a complete annual cycle in three millennia-old Antarctic lakes and a near-shore marine site. By establishing what the microbes do in different seasons, he noted in his proposal, he and his colleagues hope to learn which microbial processes change and about the factors that control the evolution and speciation of marine-derived communities in cold environments.

With samples collected from surface waters down to the deep ocean, Steve Hallam from Canada’s University of British Columbia will explore metabolic pathways and compounds involved in marine carbon cycling processes to understand how carbon is regulated in the oceans.

The project of Hans-Peter Klenk, of DSMZ in Germany, will generate sequences of 1,000 strains of Actinobacteria, which represent the third most populated bacterial phylum and look for genes that encode cellulose-degrading enzymes or enzymes involved in synthesizing novel, natural products.

Han Wosten of the Netherlands’ Utrecht University will carry out a functional genomics approach to wood degradation by looking at Agaricomycetes, in particular the model white rot fungus Schizophyllum commune and the more potent wood-degrading white rots Phanaerochaete chrysosporium and Pleurotus ostreatus that the DOE JGI has previously sequenced.

Wen-Tso Liu of the University of Illinois and his colleagues want to understand the microbial ecology in anaerobic digesters, key components of the wastewater treatment process. They will study microbial communities in anaerobic digesters from the United States, East Asia and Europe to understand the composition and function of the microbes as they are harnessed for this low-cost municipal wastewater strategy efficiently removes waster and produces methane as a sustainable energy source.

Another project that involves wastewater, albeit indirectly, comes from Erica Young of the University of Wisconsin. She has been studying algae grown in wastewater to track how they use nitrogen and phosphorus, and how cellulose and lipids are produced. Her CSP project will characterize the relationship between the algae and the bacteria that help stabilize these algal communities, particularly the diversity of the bacterial community and the pathways and interactions involved in nutrient uptake and carbon sequestration.

Previous CSP projects and other DOE JGI collaborations are highlighted in some of the DOE JGI Annual User Meeting talks that can be seen here: http://usermeeting.jgi.doe.gov/past-speakers/. The 10th Annual Genomics of Energy and Environment Meeting will be held March 24-26, 2015 in Walnut Creek, Calif. A preliminary speakers list is posted here (http://usermeeting.jgi.doe.gov/) and registration will be opened in the first week of November.

New study of largely unstudied mesophotic coral reef geology

This is Platy coral representative of the US Virgin Islands mesophotic habitats. -  Photo by David Weinstein
This is Platy coral representative of the US Virgin Islands mesophotic habitats. – Photo by David Weinstein

A new study on biological erosion of mesophotic tropical coral reefs, which are low energy reef environments between 30-150 meters deep, provides new insights into processes that affect the overall structure of these important ecosystems. The purpose of the study was to better understand how bioerosion rates and distribution of bioeroding organisms, such as fish, mollusks and sponges, differ between mesophotic reefs and their shallow-water counterparts and the implications of those variations on the sustainability of the reef structure.

Due to major advancements in deeper underwater diving technology, a large renewal of interest in mesophotic reefs has pulsed through the scientific community because of their high biodiversity, vast extent, and potential refuge for shallower water reef species at risk from the impacts of climate change.

“Studying how mesophotic reefs function and thrive is especially critical now, when considering results from the new IPCC report reviewed by over 1700 expects said that coral reefs are the most vulnerable marine ecosystems on Earth to the adverse effects of climate change,” said David Weinstein, Rosenstiel School Ph.D. student and lead author of the study. “Developing effective environmental management strategies for these important reef systems requires a basic fundamental understanding of the underlining architecture that supports and creates diverse biological ecosystems.”

Weinstein and his research team used previously identified mesophotic reefs at 30-50 meters deep located in the U.S. Virgin Islands composed of a surprising number of coral growing on top different types of reef structures (patches, linear banks, basins) to better understand the role sedimentary processes have in creating and maintaining so many different structures that are critical for maximizing the biodiversity and health of the ecosystem. Researchers analyzed coral rubble and coral skeleton discs collected after one and two years of exposure to determine the sources and rates of bioerosion at these reefs.

Results of the study found that the architecturally unique structures in the study area experience significantly different bioerosion rates.

“This has very important implications when trying to predict how these reefs will grow over time and where preservation efforts might be most effective,” said Weinstein.

Although erosion of the coral skeleton disks at the very deepest sites was more uniform, the researchers suggest that this is likely because the substrates used in the study were all of uniform composition, unlike the diverse composition of the sites. These results imply that bioerosional processes at these depths still exaggerate differences in reef structure depending on the amount of living and dead coral at each reef, the amount of time that material is exposed on the surface, and different localized current flows experienced.

The study also confirmed important concepts in coral geology research that lacked proof from studies venturing deeper than 35 meters. Coral reef bioerosion in the U.S. Virgin Islands and potentially in most of the Caribbean does generally decreases with depth. This result stems from the finding that parrotfish are now the most significant bioeroding group from shallow reefs down to a mesophotic reef transition zone identified by Weinstein at 30-35 meters in depth. The study also was able to conclude bioeroding sponges are the primary organisms responsible for long-term structural modification of mesophotic reefs beyond the transitional zone.

“Coral reefs are essentially a thin benthos veneer draped upon a biologically produced inorganic three-dimensional foundation that creates habitats for many marine organisms,” said Weinstein. “Since mesophotic reefs grow so much slower than shallower reefs, identifying the sources and rate of erosion on mesophotic reefs is even more important to understand the long-term structural sustainability of these tropical reefs systems.”

However, Weinstein suggests that other processes, such as coral growth rates and cementation, must also be more fully studied before scientists have a complete understanding of mesophotic coral reefs.

The paper, currently available online and scheduled for print in a special coral reef edition of the journal Geomorphology later this summeris one of the first to address mesophotic reef sedimentology.

Mystery of before 370 Ma coral-stromatoporoid reef disappearing from the planet Earth

This shows invading bacteria-algae (yellow arrows) in the Devonian reef-building corals. -  ©Science China Press
This shows invading bacteria-algae (yellow arrows) in the Devonian reef-building corals. – ©Science China Press

The coral-stromatoporoid reef disappearing from the planet earth was one of the most significant and representative phenomena for the Late Devonian F-F transitional mass extinction event. Professor GONG Yiming and his group (Wu Yibu, Feng Qi etc.) from State Key Laboratory of Biogeology and Environmental Geology of China University of Geosciences are trying to tackle this problem. After several years of continuous research, they have discovered that blooming and invading of bacteria and algae played an important role for before 370 Ma (Late Devonian F-F transition) coral-stromatoporoid reef disappearing from the planet earth. And this may be the key that unlock mystery of the modern reef-building coral bleaching. Their work, entitled “blooming of bacteria and algae is a biokiller for mass-extinction of Devonian coral-stromatoporoid reef ecosystems”, was published in SCIENCE CHINA Earth Sciences, 2013, Vol. 56, No.7.

Modern coral reefs are widespread in tropical and subtropical shallow sea, while coral-stromatoporoid reefs were much more widespread and spectacular before 370 Ma. But the former keep reducing because of reef-building corals bleaching; while the latter were extincted before 370 Ma. Why these happened? Are there any relationships between them? Bacteria and algae may be the most potent killer for both of them.

The innovation of this study is that evidences of direct interactions between bacteria and algae and living reef-building coral-stromatoporoids in the Devonian fossil records have been found in terms of the relationships between organisms and environments, as well as interactions between microbes and macro-organisms. These evidences include many kinds of invading bacteria and algae in “living” Devonian reef-builders in thin sections (as shown in the Figure 1). Bacteria and algae prevented growth of coral-stromatoporoids and the latter had the ability of self-healing(as shown in the Figure 2). Hence they suggested that blooming and invading of bacteria and algae was a possible biokiller for before 370 Ma coral-stromatoporoid reef disappearing from the planet earth. It is worth noting that similar phenomena have been widely reported in modern coral reefs.
This study may give the key to unlock mystery of the modern reef-building coral bleaching and also provide a warning and revelation in prevention and treatment of modern coral reef bleaching.

Natural Ocean ‘Thermostat’ May Protect Some Coral Reefs





The Western Pacific Warm Pool, which lies northeast of Australia, contains some of the warmest ocean waters in the world. Water temperatures in the warm pool have risen less than elsewhere in the tropics, which may explain why reefs there have experienced less coral bleaching. - Illustration by Steve Deyo, ©UCAR
The Western Pacific Warm Pool, which lies northeast of Australia, contains some of the warmest ocean waters in the world. Water temperatures in the warm pool have risen less than elsewhere in the tropics, which may explain why reefs there have experienced less coral bleaching. – Illustration by Steve Deyo, ©UCAR

Natural processes may prevent oceans from warming beyond a certain point, helping protect some coral reefs from the impacts of climate change, new research finds. The study, by scientists at the National Center for Atmospheric Research (NCAR) and Australian Institute of Marine Science (AIMS), finds evidence that an ocean “thermostat” appears to be helping to regulate sea-surface temperatures in a biologically diverse region of the western Pacific.



The research will be published online Saturday in Geophysical Research Letters. It was funded by the National Science Foundation, NCAR’s primary sponsor, with support from the U.S. Department of Energy; the Japanese Ministry of Education, Culture, Sports, Science, and Technology; and AIMS.



The research team, led by NCAR scientist Joan Kleypas, looked at the Western Pacific Warm Pool, a region northeast of Australia where naturally warm sea-surface temperatures have risen little in recent decades. As a result, the reefs in that region appear to have suffered relatively few episodes of coral bleaching, a phenomenon that has damaged reefs in other areas where temperature increases have been more pronounced.



The study lends support to a much-debated theory that a natural ocean thermostat prevents sea-surface temperatures from exceeding about 88 degrees Fahrenheit (31 degrees Celsius) in open oceans. If so, this thermostat would protect reefs that have evolved in naturally warm waters that will not warm much further, as opposed to reefs that live in slightly cooler waters that face more significant warming.



“Global warming is damaging many corals, but it appears to be bypassing certain reefs that support some of the greatest diversity of life on the planet,” Kleypas says. “In essence, reefs that are already in hot water may be more protected from warming than reefs that are not. This is some rare hopeful news for these important ecosystems.”

Coral bleaching: The warm pool exception



Coral reefs face a multitude of threats, including overfishing, coastal development, pollution, and changes to ocean chemistry caused by rising levels of carbon dioxide in the atmosphere. But global warming presents a particularly grave threat because unusually warm ocean temperatures can lead to episodes of coral bleaching, in which corals turn white after expelling the colorful microscopic algae that provide them with nutrition. Unless cooler temperatures return in a few days or weeks, allowing algae to grow again, bleached corals often collapse and die.



Bleaching can occur naturally, but it has become increasingly widespread in recent decades. This is largely because sea-surface temperatures in tropical waters where corals live have increased about 0.5-0.7 degrees Fahrenheit (0.3-0.4 degrees Celsius) over the last two to three decades, with temperatures occasionally spiking higher.



However, between 1980 and 2005, only four episodes of bleaching have been reported for reefs in the Western Pacific Warm Pool. This is a lower rate than any other reef region, even though the western Pacific reefs appear to be especially sensitive to temperature changes. Sea-surface temperatures in the warm pool naturally average about 84 degrees Fahrenheit (29 degrees Celsius), which is close to the proposed thermostat limit. They have warmed up about half as much as in cooler areas of the oceans.



To study the correlation between temperatures and bleaching, the authors analyzed sea-surface temperatures from the period 1950-2006 in tropical waters that are home to corals, relying on measurements taken by ships, buoys, and satellites. They also used the NCAR-based Community Climate System Model to study computer simulations of past and future sea-surface temperatures. The team compared the actual and simulated temperatures to a database of coral bleaching reports, mostly taken from 1980 to 2005.


Will more warming raise the thermostat?



Researchers have speculated about several processes that could regulate ocean temperatures. As surface waters warm, more water evaporates, which can increase cloud cover and winds that cool the surface. In some areas, warming alters ocean currents in ways that bring in cooler waters. In addition, the very process of evaporation removes heat.



“This year, 2008, is the International Year of the Reef, and we need to go beyond the dire predictions for coral reefs and find ways to conserve them,” Kleypas says. “Warming waters are just one part of the picture, but they are an important part. As we evaluate how and where to protect reefs, we need to determine whether the ocean thermostat offers some protection against coral bleaching.”



Kleypas and her co-authors say more research needs to be conducted on the thermostat. In particular, scientists are uncertain whether global warming may alter it, raising the upper limit for sea-surface temperatures. Computer model simulations tend to capture the slow rate of warming in the western Pacific over the last few decades, but they show the warm pool heating rapidly in the future.



“Computer models of Earth’s climate show that sea-surface temperatures will rise substantially this century,” says NCAR scientist Gokhan Danabasoglu, a co-author of the study. “Unfortunately, these future simulations show the Western Pacific Warm Pool warming at a similar rate as the surrounding areas instead of being constrained by a thermostat. We don’t know if the models are simply not capturing the processes that cause the thermostat, or if global warming is happening so rapidly that it will overwhelm the thermostat.”